A Smoothing Newton-BICGStab Method for Least Squares Matrix Nuclear Norm Problems

Master'sMASTER OF SCIENC

A Category of Genes

Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our ability to integrate various aspects of the gene functions and view the genome holistically. To overcome these limitations, we need a more appropriate way to describe the intricate relationships between genes. Interestingly, category theory, an abstract field of mathematics seemingly unrelated to biology, has emerged as a powerful language for describing relations in general. We propose that category theory could provide a framework for unifying our knowledge of genes and their relationships. As a starting point, we construct a category of genes, with its morphisms abstracting various aspects of the relationships betweens genes. These relationships include, but not limited to, the order of genes on the chromosomes, the physical or genetic interactions, the signalling pathways, the gene ontology causal activity models (GO-CAM) and gene groups. Previously, they were encoded by miscellaneous networks or graphs, while our work unifies them in a consistent manner as a category. By doing so, we hope to view the relationships between genes systematically. In the long run, this paves a promising way for us to understand the fundamental principles that govern gene regulation and function.Comment: 13 pages, 6 figures, 1 tabl